Course catalogue doctoral education - VT24
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| Title | Microscopy: Improve Your Imaging Skills - From Sample Preparation to Image Analysis |
|---|---|
| Course number | 2870 |
| Programme | Utveckling och regeneration (DevReg) |
| Language | English |
| Credits | 6.0 |
| Date | 2024-01-29 -- 2024-02-16 | Responsible KI department | Institutionen för biovetenskaper och näringslära |
| Specific entry requirements | The applicants must a) have an active microscopy project involving imaging of a fluorescent sample, started minimum 3 months prior to the start of the course; b) be able to prepare their sample and bring it to the course; c) In their lab or local facility, have been trained on and have regularly used a microscope able to acquire images of fluorescent samples d) have access to that microscope during the course (some assignments require submitting new images); e) set aside time so they can be fully committed to the course for 3 weeks, including the equivalent of about 2 days of work before the course (includes preparing their samples). The applications must contain the following 4 parts: 1) the confirmation that the applicants fulfil the a, b, c, d and e conditions listed above; 2) a brief description of the scientific aim of their own imaging projects; 3) a brief description of their microscopy experience so far, when they started their current microscopy project and which microscope(s) they currently use; 4) fluorescent images of their sample acquired by them on the microscope mentioned above and submitted in the original format delivered by the microscope (please write to Anna Wallén (Anna.Wallen@ki.se) to ask for a link to upload your original images). Applications will only be considered when all these 4 points are present. Researchers who have not yet used microscopy or do not have an active microscopy project are advised to get trained at their local imaging facility, actively acquire images for at least 3 months then apply to the LCI course next year. |
| Purpose of the course | The aim of this course is to enable PhD students and researchers who have recently acquired images of fluorescent samples but feel insecure about their microscopy skills and knowledge, to become proficient in designing and performing microscopy for their OWN project.
The course is NOT aimed at training people to use the LCI facility microscopes. The focus is instead on enabling the students to acquire enough theoretical and practical knowledge to 1) make their scientific question compatible with extracting data from fluorescence images, 2) assess and if needed improve the preparation of their OWN sample to help reliable extraction of meaningful data, 3) assess and if needed improve the imaging settings in their OWN software and on their OWN microscope, available in their lab/facility. The aim of the course is to provide the students with the tools to acquire on ANY wide field, confocal or light sheet microscope, images of their samples that reliably answer their scientific question. |
| Intended learning outcomes | At the end of the course, the participants should be able to:
1- Scientific question: Formulate their scientific question in terms of which parameters in the image need to be measured and which image resolution is required to enable this measurement. 2- Sample preparation: Assess how their own sample corresponds to/deviates from a perfect sample for light microscopy, justify why they are preparing their sample the way they do, and infer what they can do to improve it. 3- Microscope: Explain how their own microscope works and argue why this is the most suitable type of microscope to answer their scientific question, or why a different type of microscope would be more adequate. 4- Objective: Justify why the objective they use is adequate to answer their scientific question or why another objective would work better. 5- Sampling: Calculate if the pixel size in their images fulfils the Nyquist sampling theorem, explain why this is appropriate for their experiment or which sampling settings would work better. 6- Artifacts: Identify typical pitfalls that prevent reliable data extraction from microscopy images (saturation, bleedthrough, undersampling), explain why they are a problem and which settings can be adjusted to avoid them. |
| Contents of the course | The course content covers the whole process of producing scientific results for an experiment requiring light microscopy: formulation of the scientific question, sample preparation, choice of microscope, objective and settings for acquisition, image format and management, image processing for data extraction, preparation of figures and text for publication, ethics.
The course is fully designed so that, during the course, the students apply all the points above to their OWN project, sample and equipment. The students never use the microscopes at our facility. Aside from the points described in the Learning Outcomes, the participants will be able to learn the following: - The differences (theory and hardware) between wide field, confocal and light sheet microscopes as well as the different types of confocal microscopes - How to pick the best combination of fluorophores for their own sample on their own microscope, identify and eliminate bleed-through and cross-excitation problems - How to find the area of interest in their sample without bleaching it - How to adjust the condenser for proper transmitted light imaging - How to set the following microscope parameters: resolution, pixel size, averaging, scan speed, illumination power, detector gain and offset, camera readout rate, exposure time and binning - Many practical tricks about fixation, mounting and handling of their sample in a way that is optimal for imaging - How to deal with the challenges of imaging fluorescent volumes - What hardware or software autofocus, spectral detector, resonance scanner, two-photon or super resolution microscopy are used for - Many personalized tips on how to improve the preparation and imaging of their own sample on their own microscope (through the workshop where we will image their own sample) - Where to get help to create an image analysis pipeline for their own images and scientific question - The ethics of handling scientific images for publication - How to easily assemble a figure for publications |
| Teaching and learning activities | Lectures, videos, workshops, group discussions, project presentations, quizzes, assignments and portfolio. The students must prepare their own sample before the course starts and need to plan accordingly. The course is intensive and requires a few days of work before the course starts as well as a few days afterwards to prepare and submit the final portfolio. |
| Compulsory elements | Attendance to all sessions is compulsory. Any absence must be reported to the course leader in advance by e-mail. Absence from any part of the course (lectures, laboratory sessions, discussion sessions and exam) is generally not accepted but could in exceptional cases be compensated by a written additional assignment to ensure the learning outcomes of the day have been reached. If it is not possible to compensate, the student will be given the chance to complete the course by attending the missing sessions the following year. |
| Examination | The final mark (pass or fail) will depend on the way the students demonstrate in the daily, weekly and final portfolio assignments that they have reached the Intended Learning Outcomes. |
| Literature and other teaching material | Reference literature: Handbook of Biological confocal microscopy, James Pawley Springer Editions 2006 (PDF file available at the KI library) |
| Number of students | 12 - 20 |
| Selection of students | The selection will be based on the applicants' project and recent microscopy experience, their potential to follow the course and fulfil the imaging assignments, and the usefulness of the course to their current research project. |
| More information | This is an intensive course. Do not plan any experiments or meetings during the 3 weeks of the course itself. Plan to need some time before and after the course. If you have several projects, describe only the most relevant in the application and prepare the corresponding sample for the course. |
| Additional course leader | In case of problem with the application process, please contact Anna Wallén (anna.wallen@ki.se). |
| Latest course evaluation | Course evaluation report |
| Course responsible |
Sylvie Le Guyader Institutionen för biovetenskaper och näringslära Sylvie.Le.Guyader@ki.se |
| Contact person | - |
